From what I understand, they do this a lot in every game. They didn't stop doing it to me until I conquered their CoT.
I have a question. How do you excommunicate someone as the Papal Controller? I can't find the option anywhere.
it's among the other diplomatic actions (declare war, royal marriage etc.) - the very last of them IIRC. however the target must have low Papal Influence and relations worse than +100 with the Papal State to allow you doing that.